Assign VM after un-publshing to the owner

Make sure that we unpublish public virtual study. Fail otherwise.

docs/Create-And-Publish-Virtual-Study.md

@@ -49,7 +49,8 @@ Specifying the `pmid` enables a link to the PubMed page of the study.
 ## Un-publish Virtual Study
 
 To un-publish a virtual study, you need to supply the publisher API key in the `X-PUBLISHER-API-KEY` header.
-After un-publishing, the virtual study is still accessible by the link, but it will be unlisted from the list of public virtual studies and not shown on the landing page anymore.
+After un-publishing, virtual study will no longer be displayed in the `Public Virtual Studies` section on the landing page.
+However, it reappears in the `My Virtual Studies` section for the owner.
 
 Here is the command to un-publish a virtual study:
 ```shell

src/main/java/org/cbioportal/web/PublicVirtualStudiesController.java

@@ -24,6 +24,7 @@
 import org.springframework.web.bind.annotation.RequestParam;
 
 import java.util.List;
+import java.util.NoSuchElementException;
 import java.util.Set;
 
 @Controller
@@ -72,15 +73,21 @@ public ResponseEntity<Void> publishVirtualStudy(
 
     @DeleteMapping("/{id}")
     @ApiResponse(responseCode = "200", description = "OK")
-    public ResponseEntity<Void> retractVirtualStudy(
+    public ResponseEntity<Void> unPublishVirtualStudy(
         @PathVariable String id,
         @RequestHeader(value = "X-PUBLISHER-API-KEY") String providedPublisherApiKey
     ) {
         ensureProvidedPublisherApiKeyCorrect(providedPublisherApiKey);
-        sessionServiceRequestHandler.softRemoveVirtualStudy(id);
+        unPublishVirtualStudy(id);
         return ResponseEntity.ok().build();
     }
 
+    /**
+     * Publishes virtual study optionally updating metadata fields
+     * @param id - id of public virtual study to publish
+     * @param typeOfCancerId - if specified (not null) update type of cancer of published virtual study
+     * @param pmid  - if specified (not null) update PubMed ID of published virtual study
+     */
     private void publishVirtualStudy(String id, String typeOfCancerId, String pmid) {
         VirtualStudy virtualStudyDataToPublish = sessionServiceRequestHandler.getVirtualStudyById(id);
         VirtualStudyData virtualStudyData = virtualStudyDataToPublish.getData();
@@ -89,6 +96,24 @@ private void publishVirtualStudy(String id, String typeOfCancerId, String pmid)
         sessionServiceRequestHandler.updateVirtualStudy(virtualStudyDataToPublish);
     }
 
+    /**
+     * Un-publish virtual study
+     * @param id - id of public virtual study to un-publish
+     */
+    private void unPublishVirtualStudy(String id) {
+        VirtualStudy virtualStudyToUnPublish = sessionServiceRequestHandler.getVirtualStudyById(id);
+        if (virtualStudyToUnPublish == null) {
+            throw new NoSuchElementException("The virtual study with id=" + id + " has not been found in the public list.");
+        }
+        VirtualStudyData virtualStudyData = virtualStudyToUnPublish.getData();
+        Set<String> users = virtualStudyData.getUsers();
+        if (users == null || users.isEmpty() || !users.contains(ALL_USERS)) {
+            throw new NoSuchElementException("The virtual study with id=" + id + " has not been found in the public list.");
+        }
+        virtualStudyData.setUsers(Set.of(virtualStudyData.getOwner()));
+        sessionServiceRequestHandler.updateVirtualStudy(virtualStudyToUnPublish);
+    }
+
     private void ensureProvidedPublisherApiKeyCorrect(String providedPublisherApiKey) {
         if (requiredPublisherApiKey.isBlank()
             || !requiredPublisherApiKey.equals(providedPublisherApiKey)) {

src/main/java/org/cbioportal/web/error/GlobalExceptionHandler.java

@@ -18,6 +18,7 @@
 import org.springframework.web.bind.annotation.ExceptionHandler;
 
 import java.util.Iterator;
+import java.util.NoSuchElementException;
 
 
 // TODO
@@ -207,4 +208,9 @@ public ResponseEntity<ErrorResponse> handleBadSqlGrammar(BadSqlGrammarException
             HttpStatus.INTERNAL_SERVER_ERROR
         );
     }
+
+    @ExceptionHandler(NoSuchElementException.class)
+    public ResponseEntity<ErrorResponse> handleNoSuchElementException(NoSuchElementException ex) {
+        return new ResponseEntity<>(new ErrorResponse(ex.getMessage()), HttpStatus.NOT_FOUND);
+    }
 }

src/test/java/org/cbioportal/test/integration/PublicVirtualStudiesIntegrationTest.java

@@ -109,6 +109,16 @@ public void test2CreateVirtualStudy() {
         virtualStudyId = savedVs.getId();
     }
 
+    @Test
+    public void test2_1UnPublishVirtualStudyFails() {
+        ResponseEntity<Object> response = restTemplate.exchange(
+            CBIO_URL + "/api/public_virtual_studies/" + virtualStudyId,
+            HttpMethod.DELETE,
+            new HttpEntity<>(null, validKeyContainingHeaders),
+            Object.class);
+        assertThat(response.getStatusCode()).isEqualTo(HttpStatus.NOT_FOUND);
+    }
+
     @Test
     public void test3PublishVirtualStudy() {
         String url = CBIO_URL + "/api/public_virtual_studies/" + virtualStudyId + "?typeOfCancerId=acc&pmid=12345";
@@ -158,28 +168,28 @@ public void test4ListJustPublishedStudy() {
 
     @Test
     public void test5UnpublishVirtualStudy() {
-        ResponseEntity<Object> response5 = restTemplate.exchange(
+        ResponseEntity<Void> response5 = restTemplate.exchange(
             CBIO_URL + "/api/public_virtual_studies/" + virtualStudyId,
             HttpMethod.DELETE,
             null,
-            Object.class);
+            Void.class);
         assertThat(response5.getStatusCode()).isEqualTo(HttpStatus.BAD_REQUEST);
 
         response5 = restTemplate.exchange(
             CBIO_URL + "/api/public_virtual_studies/" + virtualStudyId,
             HttpMethod.DELETE,
             new HttpEntity<>(null, invalidKeyContainingHeaders),
-            Object.class);
+            Void.class);
         assertThat(response5.getStatusCode()).isEqualTo(HttpStatus.UNAUTHORIZED);
 
         response5 = restTemplate.exchange(
             CBIO_URL + "/api/public_virtual_studies/" + virtualStudyId,
             HttpMethod.DELETE,
             new HttpEntity<>(null, validKeyContainingHeaders),
-            Object.class);
+            Void.class);
         assertThat(response5.getStatusCode().is2xxSuccessful()).isTrue();
     }
-    
+
     @Test
     public void test6NoPublicVirtualStudiesAfterRemoval() {
         ResponseEntity<List<VirtualStudy>> response6 = restTemplate.exchange(
@@ -192,6 +202,18 @@ public void test6NoPublicVirtualStudiesAfterRemoval() {
         assertThat(response6.getBody()).isEmpty();
     }
 
+    @Test
+    public void test7UnpublishedVirtualStudyExists() {
+        ResponseEntity<VirtualStudy> response = restTemplate.exchange(
+            CBIO_URL + "/api/session/virtual_study/" + virtualStudyId,
+            HttpMethod.GET,
+            null,
+            VirtualStudy.class);
+        assertThat(response.getStatusCode()).isEqualTo(HttpStatus.OK);
+        VirtualStudy body = response.getBody();
+        assertThat(body).isNotNull();
+    }
+
     static VirtualStudyData createTestVsData() {
         VirtualStudyData data = new VirtualStudyData();
         data.setName("test virtual study name");